| URL: | http://www.polebio.lrsv.ups-tlse.fr/ProtAnnDB/ |
| Full name: | Protein Annotation DataBase |
| Description: | To facilitate interpretation of proteomic and transcriptomic data, ProtAnnDB (Protein Annotation DataBase) collects predictions of sub-cellular localization and functional domains made by available software and provides scores to assess the quality of these predictions. |
| Year founded: | 2009 |
| Last update: | 2018-07-10 |
| Version: | 9th |
| Accessibility: |
Accessible
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| Country/Region: | France |
| Data type: | |
| Data object: | |
| Database category: | |
| Major species: |
Arabidopsis thaliana
Brachypodium distachyon
Eucalyptus grandis
Oryza sativa
Solanum tuberosum
Solanum lycopersicum
Malus domestica
Medicago truncatula
Populus trichocarpa
Linum usitatissimum
Gossypium raimondii
Helianthus annuus
Sorghum bicolor
Glycine max
Triticum aestivum
Zea mays
Marchantia polymorpha
Physcomitrella patens
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| Keywords: |
| University/Institution: | University of Toulouse |
| Address: | LRSV (Plant Science Research Laboratory, UMR 5546 UPS/CNRS) 24 chemin de Borderouge -Auzeville BP 42617 31326 Castanet-Tolosan Cedex France |
| City: | |
| Province/State: | |
| Country/Region: | France |
| Contact name (PI/Team): | Elisabeth Jamet |
| Contact email (PI/Helpdesk): | jamet@lrsv.ups-tlse.fr |
|
Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case. [PMID: 20140071]
Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control). |